#METABOLOMICS WORKBENCH lai_yunjia_20241124_130943 DATATRACK_ID:5391 STUDY_ID:ST003594 ANALYSIS_ID:AN005902 PROJECT_ID:PR002222 VERSION 1 CREATED_ON November 25, 2024, 6:34 pm #PROJECT PR:PROJECT_TITLE Comparative metabolomics of a-Synuclein expression in Drosophila melanogaster PR:PROJECT_TYPE untargeted metabolomics PR:PROJECT_SUMMARY Drosophila melanogaster, or the fruit fly, is a great model system for motor PR:PROJECT_SUMMARY disorders such as Parkinson’s disease (PD). However, Drosophila does not PR:PROJECT_SUMMARY express in vivo the α-Synuclein (αSyn) protein, the chief molecular hallmark PR:PROJECT_SUMMARY of PD. Therefore, αSyn-expression in Drosophila and profiling the associated PR:PROJECT_SUMMARY metabolomic changes are crucial in elucidating molecular mechanism of PD using PR:PROJECT_SUMMARY Drosophila models. Using comparative global metabolomics and integrated PR:PROJECT_SUMMARY cheminformatics for high coverage, this study aims to provide fundamental PR:PROJECT_SUMMARY metabolomics data specific to αSyn expression in Drosophila melanogaster. Fly PR:PROJECT_SUMMARY heads and body compartments were analyzed separately, with an interest to probe PR:PROJECT_SUMMARY the gut-brain axis potentially involved. PR:INSTITUTE Columbia University PR:DEPARTMENT Department of Environmental Health Sciences PR:LABORATORY The Miller Lab PR:LAST_NAME Lai PR:FIRST_NAME Yunjia PR:ADDRESS 630 West 168th Street, P&S 16-421, New York, NY 10032 PR:EMAIL yunjia.lai@outlook.com PR:PHONE 9194805489 #STUDY ST:STUDY_TITLE Metabolomics of Drosophila melanogaster with a-Synuclein expression (body) ST:STUDY_TYPE untargeted metabolomics ST:STUDY_SUMMARY High-coverage LC-HRMS metabolomics were applied to profiling αSyn-expressing ST:STUDY_SUMMARY flies vs. wild-type flies. Fly heads and bodies were extracted and analyzed ST:STUDY_SUMMARY using liquid chromatography–quadrupole-orbitrap mass spectrometry, following ST:STUDY_SUMMARY informatics approaches for compound identification and pathway analysis. The ST:STUDY_SUMMARY uploaded is the untargeted metabolomics component which contains raw data, ST:STUDY_SUMMARY alignment tables, and associated method details. This study provides comparative ST:STUDY_SUMMARY data for fly body. ST:INSTITUTE Columbia University ST:DEPARTMENT Department of Environmental Health Sciences ST:LAST_NAME Lai ST:FIRST_NAME Yunjia ST:ADDRESS 630 West 168th Street, P&S 16-421, New York, NY 10032 ST:EMAIL yunjia.lai@outlook.com ST:PHONE 9194805489 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 100; five samples per group; 10 subjects per sample ST:NUM_MALES 100; five samples per group; 10 subjects per sample #SUBJECT SU:SUBJECT_TYPE Insect SU:SUBJECT_SPECIES Drosophila melanogaster SU:TAXONOMY_ID 7227 SU:GENOTYPE_STRAIN alpha-synuclein; wild-type SU:AGE_OR_AGE_RANGE adult SU:GENDER Male #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - body_Pos_xCB1 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xCB1.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xCB2 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xCB2.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xCB3 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xCB3.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xCB4 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xCB4.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xCB5 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xCB5.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xSB1 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xSB1.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xSB2 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xSB2.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xSB3 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xSB3.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xSB4 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xSB4.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_xSB5 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_xSB5.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_bQCinj1 Genotype:n/a | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_bQCinj1.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_bQCinj2 Genotype:n/a | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_bQCinj2.mzXML SUBJECT_SAMPLE_FACTORS - body_Pos_bQCinj3 Genotype:n/a | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Pos_bQCinj3.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xCB1 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xCB1.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xCB2 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xCB2.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xCB3 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xCB3.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xCB4 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xCB4.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xCB5 Genotype:Wild-type, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xCB5.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xSB1 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xSB1.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xSB2 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xSB2.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xSB3 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xSB3.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xSB4 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xSB4.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_xSB5 Genotype:aSyn expression, red eye | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_xSB5.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_bQCinj1 Genotype:n/a | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_bQCinj1.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_bQCinj2 Genotype:n/a | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_bQCinj2.mzXML SUBJECT_SAMPLE_FACTORS - body_Neg_bQCinj3 Genotype:n/a | Sample source:fly body RAW_FILE_NAME(raw data file names)=body_Neg_bQCinj3.mzXML #COLLECTION CO:COLLECTION_SUMMARY age-matched adult fruit fly with heads and bodies separated for comparative CO:COLLECTION_SUMMARY metabolomics of alpha-synuclein vs. wild-type control CO:SAMPLE_TYPE fly body #TREATMENT TR:TREATMENT_SUMMARY This is a baseline profiling for genotypes αSyn-expression vs. wild-type in TR:TREATMENT_SUMMARY Drosophila melanogaster. No treatment was involved. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Age-matched adult flies were used, with each genotypic group containing five SP:SAMPLEPREP_SUMMARY sample replicates, and each replicate sample ten heads/bodies. To extract SP:SAMPLEPREP_SUMMARY metabolites, thawed heads and bodies were added with ice-cold methanol:H2O (2:1, SP:SAMPLEPREP_SUMMARY v/v) solution pre-spiked with isotope-labeled internal standards alongside SP:SAMPLEPREP_SUMMARY zirconium oxide beads (0.5 mm i.d., Yittria stabilized) (Next Advance, Troy, SP:SAMPLEPREP_SUMMARY NY). Samples were touch vortexed for 30 sec, manually ground using sterile, SP:SAMPLEPREP_SUMMARY disposable pestles (DWK Life Sciences, Millville, NJ), placed on a bead beater SP:SAMPLEPREP_SUMMARY (Next Advance, Troy, NY) in a cold room for 5 mins at the maximum speed, and SP:SAMPLEPREP_SUMMARY finally centrifuged at 18,000 × g for 10 mins. The supernatant was SP:SAMPLEPREP_SUMMARY SpeedVac-dried and reconstituted into acetonitrile:H2O (2:98, v/v) upon SP:SAMPLEPREP_SUMMARY instrumental analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Thermo Vanquish CH:COLUMN_NAME Waters ACQUITY UPLC HSS C18 (100 x 2.1mm,1.8um) CH:SOLVENT_A 100% Water; 0.1% formic acid CH:SOLVENT_B 100% Acetonitrile; 0.1% formic acid CH:FLOW_GRADIENT a 15-min gradient: 2% B, 0–1 min; 2 to 15% B, 1–3 min; 15 to 50% B, 3–6 CH:FLOW_GRADIENT min; 50 to 98% B, 6–7.5 min; 98% B, 7.5–11.5 min; 98 to 2% B, 11.5–11.6 CH:FLOW_GRADIENT min; 2% B, 11.6–15 min. CH:FLOW_RATE 0.4 mL/min CH:COLUMN_TEMPERATURE 40°C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Orbitrap IQ-X Tribrid MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS Data in both heated ESI positive and negative modes were acquired. Quality MS:MS_COMMENTS assurance and quality control (QA/QC) procedures were implemented, spanning MS:MS_COMMENTS timely mass calibration, sample blindfolding, sample randomization, and internal MS:MS_COMMENTS standard-based monitoring.MS1 *.raw data were converted to *.abf, and processed MS:MS_COMMENTS in MS-DIAL 4.90 (Riken, Japan) to obtain peak alignment tables separately for MS:MS_COMMENTS the head (ESI+), head (ESI-), body (ESI+), and body (ESI-) modes of analysis; MS:MS_COMMENTS detailed settings for data processing can be found in the SI Appendix. Welch's MS:MS_COMMENTS t-test and one-way ANOVA were performed on each of the four datasets to screen MS:MS_COMMENTS for ion features of statistical significance; retrospectively, tandem MS/MS mass MS:MS_COMMENTS spectra were collected for these features correspondingly using pooled samples, MS:MS_COMMENTS separately for fly heads and bodies. MS:MS_RESULTS_FILE ST003594_AN005902_Results.txt UNITS:Peak intensity (area) Has m/z:Yes Has RT:Yes RT units:Minutes #END